As reported here:
If you encounter this bug too, please don't post a new question about it. Feel free to comment in this thread to let us know you have also had the same problem. Tell us what version of the GATK you were using and post your command line.
Thank you for your patience while we work to fix this issue.
Update: it seems the cases in the different tools aren't directly related. The PrintReads and HaplotypeCaller cases are now solved; still waiting on test files for the UG case.